SAXSdb — 2xdm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 COBALT (II) ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 (D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 (D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 COBALT (II) ION × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAC_ACTSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–466； UniProt 50–515 Author chain B； PDBConstruct 1–466； UniProt 50–515 Author chain C； PDBConstruct 1–466； UniProt 50–515 Author chain D； PDBConstruct 1–466； UniProt 50–515

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2xdm
Deposition date deposition_date	2010-05-04
Structure title title	Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic boronate inhibitor
Keywords keywords	HYDROLASE-INHIBITOR COMPLEX, BORONIC ACID, PEPTIDOGLYCAN, HYDROLASE; HYDROLASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2xdm__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2xdm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xdm__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.20 Å
Rg (electron density)	24.26 Å
Total Rg	24.97 Å
Atom count	3385
Residues	465
Excluded volume	59121 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xdm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xdm__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xdm__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2xdm__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
Molecular weight formula_weight	47647.0 kDa
EC 编号 ec_number	3.4.16.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14096

RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONIC ACID
Molecular weight formula_weight	263.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	555

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2xdmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xdmA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

Domain ID domain_id	2xdmB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xdmB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

Domain ID domain_id	2xdmC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xdmC02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

Domain ID domain_id	2xdmD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	2xdmD02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

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Unit-cell length a length_a	103.308 Å
Unit-cell length b length_b	91.568 Å
Unit-cell length c length_c	106.871 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	32.430 Å
R factor r_factor	0.2026
R_work r_work	0.1995
R_free r_free	0.2622

Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic boronate inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2xdm__assembly_3__model_1

2xdm__assembly_3__model_1 | I(q)

2xdm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic boronate inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2xdm__assembly_3__model_1

2xdm__assembly_3__model_1 | I(q)

2xdm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)